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Time-resolved IR spectroscopy reveals mechanistic details of ion transport in the sodium pump Krokinobacter eikastus rhodopsin 2

Published on Feb 20, 2019in Physical Chemistry Chemical Physics3.567
· DOI :10.1039/C8CP07418F
Marvin Asido1
Estimated H-index: 1
(Goethe University Frankfurt),
Peter Eberhardt3
Estimated H-index: 3
(Goethe University Frankfurt)
+ 3 AuthorsJosef Wachtveitl38
Estimated H-index: 38
(Goethe University Frankfurt)
Abstract
We report a comparative study on the structural dynamics of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 wild type under sodium and proton pumping conditions by means of time-resolved IR spectroscopy. The kinetics of KR2 under sodium pumping conditions exhibits a sequential character, whereas the kinetics of KR2 under proton pumping conditions involves several equilibrium states. The sodium translocation itself is characterized by major conformational changes of the protein backbone, such as distortions of the α-helices and probably of the ECL1 domain, indicated by distinct marker bands in the amide I region. Carbonyl stretch modes of specific amino acid residues helped to elucidate structural changes in the retinal Schiff base moiety, including the protonation and deprotonation of D116, which is crucial for a deeper understanding of the mechanistic features in the photocycle of KR2.
  • References (42)
  • Citations (2)
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References42
Newest
#1Jagdeep Kaur (Goethe University Frankfurt)H-Index: 4
#2Clara Nassrin Kriebel (Goethe University Frankfurt)H-Index: 2
Last. Clemens Glaubitz (Goethe University Frankfurt)H-Index: 33
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Abstract Krokinobacter eikastus rhodopsin 2 (KR2) is a pentameric, light-driven ion pump, which selectively transports sodium or protons. The mechanism of ion selectivity and transfer is unknown. By using conventional as well as dynamic nuclear polarization (DNP)-enhanced solid-state NMR, we were able to analyse the retinal polyene chain between positions C10 and C15 as well as the Schiff base nitrogen in the KR2 resting state. In addition, 50% of the KR2 13C and 15N resonances could be assigned...
9 CitationsSource
#1Hui-Fen Chen (KMU: Kaohsiung Medical University)H-Index: 5
#2Keiichi Inoue (Nagoya Institute of Technology)H-Index: 23
Last. Hideki Kandori (Nagoya Institute of Technology)H-Index: 43
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#1Hideki KandoriH-Index: 43
#2Keiichi Inoue (National Presto Industries)H-Index: 23
Last. Satoshi P. Tsunoda (National Presto Industries)H-Index: 7
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Ion pumps perform active transport of ions by using energy. The active transport mechanism can be illustrated by the Panama Canal model, which considers two gates and a gain in energy. The Panama Canal model is consistent with the alternating access model that is used to describe active transport, in which the substrate ion is bound, energized, and released. It was generally accepted that energization occurs only for an ion-bound protein but not for an ion-unbound protein. Light-driven proton an...
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#1Carl-Mikael Suomivuori (TUM: Technische Universität München)H-Index: 7
#2Ana P. Gamiz-Hernandez (TUM: Technische Universität München)H-Index: 10
Last. Ville R. I. Kaila (TUM: Technische Universität München)H-Index: 27
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#1Thomas Köhler (Goethe University Frankfurt)H-Index: 3
#2Ingrid Weber (Goethe University Frankfurt)H-Index: 6
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The retinal protein proteorhodopsin is a homolog of the well-characterized light-driven proton pump bacteriorhodopsin. Basic mechanisms of proton transport seem to be conserved, but there are noticeable differences in the pH ranges of proton transport. Proton transport and protonation state of a carboxylic acid side chain, the primary proton acceptor, are correlated. In case of proteorhodopsin, the pKa of the primary proton acceptor Asp-97 (pKa ≈ 7.5) is unexpectedly close to environmental pH (p...
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We report femtosecond time-resolved absorption change measurements of the photoinduced deactivation dynamics of a microbial rhodopsin in the ultraviolet–visible and mid-infrared range. The blue light quenching process is recorded in green proteorhodopsin’s (GPR) primary proton donor mutant E108Q from the deprotonated 13-cis photointermediate. The return of GPR to the dark state occurs in two steps, starting with the photoinduced 13-cis to all-trans reisomerization of the retinal. The subsequent ...
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#1Rei Abe-Yoshizumi (Nagoya Institute of Technology)H-Index: 9
#2Keiichi Inoue (Nagoya Institute of Technology)H-Index: 23
Last. Hideki Kandori (Nagoya Institute of Technology)H-Index: 43
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Light-driven outward sodium-pumping rhodopsin (NaR) was recently found in marine bacteria. Krokinobacter eikastus rhodopsin 2 (KR2) actively transports sodium and lithium ions in NaCl and LiCl, respectively, while it pumps protons in KCl. NaR has a conserved NDQ (N112, D116, and Q123 in KR2) motif, and previous studies suggested an important role for N112 in the function of KR2. Here we replaced N112 with 19 different amino acids and studied the molecular properties of the mutants. All mutants e...
13 CitationsSource
#1Yusaku Hontani (VU: VU University Amsterdam)H-Index: 8
#2Keiichi Inoue (Nagoya Institute of Technology)H-Index: 23
Last. John T. M. Kennis (VU: VU University Amsterdam)H-Index: 39
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Krokinobacter rhodopsin 2 (KR2) is a recently discovered light-driven Na+ pump that holds significant promise for application as a neural silencer in optogenetics. KR2 transports Na+ (in NaCl solution) or H+ (in larger cation solution, e.g. in CsCl) during its photocycle. Here, we investigate the photochemistry of KR2 with the recently developed watermarked, baseline-free femto- to submillisecond transient stimulated Raman spectroscopy (TSRS), which enables us to investigate retinal chromophore ...
13 CitationsSource
#1Hideki Kandori (Nagoya Institute of Technology)H-Index: 43
Rhodopsins are light-sensing proteins used in optogenetics. The word “rhodopsin” originates from the Greek words “rhodo” and “opsis”, indicating rose and sight, respectively. Although the classical meaning of rhodopsin is the red-colored pigment in our eyes, the modern meaning of rhodopsin encompasses photoactive proteins containing a retinal chromophore in animals and microbes. Animal and microbial rhodopsins possess 11-cis and all-trans retinal, respectively, to capture light in seven transmem...
49 CitationsSource
#1Keiichi Inoue (Nagoya Institute of Technology)H-Index: 23
#2Masae Konno (Nagoya Institute of Technology)H-Index: 10
Last. Hideki Kandori (Nagoya Institute of Technology)H-Index: 43
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Sodium-pumping rhodopsins (NaRs) are light-driven outward Na+ pumps. NaRs have a conserved Asn, Asp, and Gln motif (NDQ) in the third transmembrane helix (helix C). The NDQ motif is thus expected to play a crucial role in the operation of the Na+ pump. Herein, we studied the photocycles of the NDQ-motif mutants of Krokinobacter rhodopsin 2 (KR2), the first discovered NaR, by flash photolysis, to obtain insight into the mechanism of Na+ transport. For example, the KR2 N112A mutant did not accumul...
22 CitationsSource
Cited By2
Newest
#1Petr SkopintsevH-Index: 8
#2D. Ehrenberg (FU: Free University of Berlin)H-Index: 4
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Light-driven sodium pumps actively transport small cations across cellular membranes1. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience. Although the resting state structures of the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been solved2,3, it is unclear how structural alterations over time allow sodium to be translocated against a concentration gradient. Here, us...
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#1Sahoko Tomida (Nagoya Institute of Technology)H-Index: 4
#2Shota Ito (Nagoya Institute of Technology)H-Index: 8
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